The First United Methodist of Apalachicola was established in 1839, making it one of the oldest churches in the state. It began as the Methodist Episcopal Church South, served by Reverend Peter Haskew, who was appointed by the Alabama/West Florida Conference to serve the St. Joseph-Apalachicola Mission. The congregation met for a time at a local hotel, then at the newly constructed Trinity Episcopal Church. They also met for several years at the homes of various members.

The first sanctuary was built and dedicated in 1846.

Early in 1900, seventy buildings, including the Methodist church, were destroyed by a fire that devastated the city. The current structure was rebuilt immediately following the fire on the same site and completed in 1901 at a cost of $3500. The Gothic and Renaissance style was typical of church architecture of the late Nineteenth and early Twentieth centuries. It was constructed with locally harvested black cypress ceilings and wainscoting and yellow pine tongue-and-groove floors and walls. The new building in 1901 boasted of electric lights, several stained glass windows and a congregation of 185 members.

The structure has been lovingly maintained by a congregation which has met there continuously since its completion, and all improvements have been appropriate to the building's style and tradition. Listed on the National Registry of Historic sites, the church receives much attention from the many visitors to the area due to its prominent location in the historic district near the downtown and has become a popular location for area weddings.